eugenefischer
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cf771ce574
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parameterized sequence indices
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2022-09-21 13:15:49 -05:00 |
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1df86f01df
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parameterized sequence indices
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2022-03-05 12:03:31 -06:00 |
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96ba57d653
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Remove singleton sequences from wells in initial filtering
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2022-03-04 16:14:17 -06:00 |
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b602fb02f1
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Remove obsolete comments
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2022-03-02 23:35:24 -06:00 |
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8275cf7740
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Check for finite pairing error rate
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2022-03-01 09:01:53 -06:00 |
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64209691f0
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Check for finite pairing error rate
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2022-03-01 09:00:58 -06:00 |
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05556bce0c
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Add units to metadata
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2022-02-27 16:08:59 -06:00 |
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a5f7c0641d
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Refactor for better encapsulation with CellSamples
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2022-02-27 14:51:53 -06:00 |
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8ebfc1469f
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Refactor plate to fill its own wells in its constructor
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2022-02-27 14:25:53 -06:00 |
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e4d094d796
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Adding GraphML output to options menu
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2022-02-24 17:22:07 -06:00 |
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8745550e11
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add MWM algorithm type to matching metadata
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2022-02-24 16:24:48 -06:00 |
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373a5e02f9
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Refactor to make CellSample class more self-contained
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2022-02-24 16:03:49 -06:00 |
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3d9890e16a
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Change GraphModificationFunctions to only save edges if graph data is cached
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2022-02-24 15:32:27 -06:00 |
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dd64ac2731
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Change GraphModificationFunctions to interface
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2022-02-24 15:18:09 -06:00 |
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8edd89d784
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Added heap type selection, fixed error handling
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2022-02-24 14:48:19 -06:00 |
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08699ce8ce
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Change output order to match interactive UI
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2022-02-23 08:56:09 -06:00 |
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e58f7b0a55
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checking for possible divide by zero error.
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2022-02-23 08:54:14 -06:00 |
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3ccee9891b
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change "concentrations" to "populations" for consistency
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2022-02-23 08:12:48 -06:00 |
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a7afeb6119
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bugfixes
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2022-02-22 22:10:09 -06:00 |
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68ee9e4bb6
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Implemented storing graphs in memory for multiple pairing experiments
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2022-02-22 21:30:00 -06:00 |
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906c06062f
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Added metadata to MatchingResult to enable CLI options
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2022-02-22 18:36:30 -06:00 |
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cb1f7adece
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Change "peptide" references in code to "sequence", adding comments
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2022-02-21 00:29:34 -06:00 |
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2023bb9d7e
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Cleanup file output, add UI verbosity
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2022-02-20 18:31:31 -06:00 |
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d1c37b5ccd
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Relocate overlap threshold filters
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2022-02-20 03:05:56 -06:00 |
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248fe4d662
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Add plate well concentrations to output data
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2022-02-20 02:09:22 -06:00 |
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5d0e60708c
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Add plate well concentrations to output data
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2022-02-20 01:53:34 -06:00 |
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c96b7237e9
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Add plate well concentrations to output data
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2022-02-20 01:40:01 -06:00 |
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0b28259800
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Add plate well concentrations to output data
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2022-02-20 01:13:22 -06:00 |
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837ef7bfe4
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UI cleanup, some code cleanup
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2022-02-20 01:05:28 -06:00 |
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0bebbc7602
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Add missing filtering code
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2022-02-19 22:56:38 -06:00 |
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c4633da9eb
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Correct propogation of peptide counts
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2022-02-19 22:33:38 -06:00 |
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5b2ed165d0
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Clean up interactive text, bugfix
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2022-02-19 22:21:09 -06:00 |
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13fb7168bf
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Refactor to read/write files of graph and map data
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2022-02-19 21:46:01 -06:00 |
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568a6be3c7
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Refactoring to allow graphs from file
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2022-02-19 17:23:55 -06:00 |
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6faacd9a82
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Adding parameters to filter by occupancy difference and percent overlap
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2022-02-19 14:05:26 -06:00 |
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47e23addfa
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Do new filtering before matching
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2022-02-18 17:42:05 -06:00 |
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b9ee31b64c
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Do new filtering before matching
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2022-02-18 17:28:24 -06:00 |
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bf32a55e4b
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Implement matching using jheaps PairingHeap
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2022-02-18 16:09:23 -06:00 |
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acff88475b
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Command line arguments working, need better documentation and error handling
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2021-11-23 12:24:48 -06:00 |
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981e24011d
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First attempt at command line arguments
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2021-11-19 17:31:18 -06:00 |
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2ab93dd4b7
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Recording source file names in output files, allowing output of intermediate results
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2021-11-18 15:38:29 -06:00 |
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34e96d3b3d
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Refactor to reduce code repetition
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2021-11-18 14:11:04 -06:00 |
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2064d7e9fc
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Implemented parameter for CDR1 frequency
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2021-11-18 11:55:54 -06:00 |
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2fee44d3ee
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removed unused imports
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2021-11-16 16:46:17 -06:00 |
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255a3ba66c
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Added timing to CDR3/CDR1 matching
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2021-11-16 16:37:29 -06:00 |
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48510a5b60
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Improved efficiency by pre-filtering peptide lists before making and processing graphs
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2021-11-16 16:31:35 -06:00 |
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26304e5dff
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bugfix
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2021-11-16 09:29:07 -06:00 |
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13b58e3204
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Expanding simulation to attempt CDR3/CDR1 matching - doubles size of cells
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2021-11-15 15:00:11 -06:00 |
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c425b05d8c
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Expanding simulation to attempt CDR3/CDR1 matching - doubles size of cells
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2021-11-15 11:24:46 -06:00 |
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92add6786a
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Bugfix, can now do plates with <96 wells
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2021-11-12 11:16:21 -06:00 |
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